[2024-01-24 13:46:56,028] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:56,034] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:56,035] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1d3301f-5d2c-42dd-ae79-c3714b664e44/dqc_reference
[2024-01-24 13:46:57,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:57,433] [INFO] Task started: Prodigal
[2024-01-24 13:46:57,433] [INFO] Running command: gunzip -c /var/lib/cwl/stg63c6df49-f111-48fe-8e25-86679340acc7/GCF_009729055.1_ASM972905v1_genomic.fna.gz | prodigal -d GCF_009729055.1_ASM972905v1_genomic.fna/cds.fna -a GCF_009729055.1_ASM972905v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:04,959] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:04,959] [INFO] Task started: HMMsearch
[2024-01-24 13:47:04,960] [INFO] Running command: hmmsearch --tblout GCF_009729055.1_ASM972905v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1d3301f-5d2c-42dd-ae79-c3714b664e44/dqc_reference/reference_markers.hmm GCF_009729055.1_ASM972905v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:05,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:05,211] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg63c6df49-f111-48fe-8e25-86679340acc7/GCF_009729055.1_ASM972905v1_genomic.fna.gz]
[2024-01-24 13:47:05,238] [INFO] Query marker FASTA was written to GCF_009729055.1_ASM972905v1_genomic.fna/markers.fasta
[2024-01-24 13:47:05,239] [INFO] Task started: Blastn
[2024-01-24 13:47:05,239] [INFO] Running command: blastn -query GCF_009729055.1_ASM972905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1d3301f-5d2c-42dd-ae79-c3714b664e44/dqc_reference/reference_markers.fasta -out GCF_009729055.1_ASM972905v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:05,735] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:05,739] [INFO] Selected 3 target genomes.
[2024-01-24 13:47:05,740] [INFO] Target genome list was writen to GCF_009729055.1_ASM972905v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:05,747] [INFO] Task started: fastANI
[2024-01-24 13:47:05,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c6df49-f111-48fe-8e25-86679340acc7/GCF_009729055.1_ASM972905v1_genomic.fna.gz --refList GCF_009729055.1_ASM972905v1_genomic.fna/target_genomes.txt --output GCF_009729055.1_ASM972905v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:09,121] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:09,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1d3301f-5d2c-42dd-ae79-c3714b664e44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:09,121] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1d3301f-5d2c-42dd-ae79-c3714b664e44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:09,127] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:47:09,127] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:09,128] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Sulfurisphaera ohwakuensis	strain=TA-1	GCA_009729055.1	69656	69656	type	True	100.0	934	934	95	conclusive
Sulfurisphaera ohwakuensis	strain=DSM 12421	GCA_014202105.1	69656	69656	type	True	99.9218	874	934	95	conclusive
Sulfurisphaera tokodaii	strain=7	GCA_000011205.1	111955	111955	type	True	94.7659	780	934	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:09,129] [INFO] DFAST Taxonomy check result was written to GCF_009729055.1_ASM972905v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:09,130] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:09,130] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:09,130] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1d3301f-5d2c-42dd-ae79-c3714b664e44/dqc_reference/checkm_data
[2024-01-24 13:47:09,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:09,170] [INFO] Task started: CheckM
[2024-01-24 13:47:09,171] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009729055.1_ASM972905v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009729055.1_ASM972905v1_genomic.fna/checkm_input GCF_009729055.1_ASM972905v1_genomic.fna/checkm_result
[2024-01-24 13:47:36,209] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:36,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:36,230] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:36,230] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:36,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009729055.1_ASM972905v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:36,231] [INFO] Task started: Blastn
[2024-01-24 13:47:36,231] [INFO] Running command: blastn -query GCF_009729055.1_ASM972905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1d3301f-5d2c-42dd-ae79-c3714b664e44/dqc_reference/reference_markers_gtdb.fasta -out GCF_009729055.1_ASM972905v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:36,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:36,690] [INFO] Selected 3 target genomes.
[2024-01-24 13:47:36,690] [INFO] Target genome list was writen to GCF_009729055.1_ASM972905v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:36,692] [INFO] Task started: fastANI
[2024-01-24 13:47:36,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c6df49-f111-48fe-8e25-86679340acc7/GCF_009729055.1_ASM972905v1_genomic.fna.gz --refList GCF_009729055.1_ASM972905v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009729055.1_ASM972905v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:39,744] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:39,749] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:39,749] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_009729055.1	s__Sulfurisphaera ohwakuensis	100.0	934	934	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfurisphaera	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000011205.1	s__Sulfurisphaera tokodaii	94.7062	783	934	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfurisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012222305.1	s__Sulfurisphaera sp012222305	90.8581	765	934	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfurisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:39,751] [INFO] GTDB search result was written to GCF_009729055.1_ASM972905v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:39,751] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:39,757] [INFO] DFAST_QC result json was written to GCF_009729055.1_ASM972905v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:39,758] [INFO] DFAST_QC completed!
[2024-01-24 13:47:39,758] [INFO] Total running time: 0h0m44s